diff --git a/include/sway/desktop/transaction.h b/include/sway/desktop/transaction.h
index 80af4aaee..dd7edb7a5 100644
--- a/include/sway/desktop/transaction.h
+++ b/include/sway/desktop/transaction.h
@@ -23,7 +23,6 @@
 
 struct sway_transaction_instruction;
 struct sway_view;
-struct sway_node;
 
 /**
  * Find all dirty containers, create and commit a transaction containing them,
@@ -31,11 +30,6 @@ struct sway_node;
  */
 void transaction_commit_dirty(void);
 
-/**
- * Remove a node that will be destroyed from transactions and dirty node lists.
- */
-void transaction_remove_node(struct sway_node *node);
-
 /*
  * Same as transaction_commit_dirty, but signalling that this is a
  * client-initiated change has already taken effect.
diff --git a/include/sway/output.h b/include/sway/output.h
index 43c3dc9ad..f6354e0ed 100644
--- a/include/sway/output.h
+++ b/include/sway/output.h
@@ -84,6 +84,8 @@ struct sway_output *output_create(struct wlr_output *wlr_output);
 
 void output_destroy(struct sway_output *output);
 
+void output_begin_destroy(struct sway_output *output);
+
 struct sway_output *output_from_wlr_output(struct wlr_output *output);
 
 struct sway_output *output_get_in_direction(struct sway_output *reference,
diff --git a/include/sway/tree/container.h b/include/sway/tree/container.h
index 4b2841042..e18fd00ac 100644
--- a/include/sway/tree/container.h
+++ b/include/sway/tree/container.h
@@ -155,6 +155,8 @@ struct sway_container *container_create(struct sway_view *view);
 
 void container_destroy(struct sway_container *con);
 
+void container_begin_destroy(struct sway_container *con);
+
 /**
  * Search a container's descendants a container based on test criteria. Returns
  * the first container that passes the test.
diff --git a/include/sway/tree/node.h b/include/sway/tree/node.h
index 7b6e936c7..e2dbcdf05 100644
--- a/include/sway/tree/node.h
+++ b/include/sway/tree/node.h
@@ -39,6 +39,7 @@ struct sway_node {
 
 	struct sway_transaction_instruction *instruction;
 	size_t ntxnrefs;
+	bool destroying;
 
 	// If true, indicates that the container has pending state that differs from
 	// the current.
diff --git a/include/sway/tree/view.h b/include/sway/tree/view.h
index d999b5024..6151a0234 100644
--- a/include/sway/tree/view.h
+++ b/include/sway/tree/view.h
@@ -101,6 +101,8 @@ struct sway_view {
 	struct wl_listener foreign_close_request;
 	struct wl_listener foreign_destroy;
 
+	bool destroying;
+
 	list_t *executed_criteria; // struct criteria *
 
 	union {
@@ -294,6 +296,8 @@ bool view_init(struct sway_view *view, enum sway_view_type type,
 
 void view_destroy(struct sway_view *view);
 
+void view_begin_destroy(struct sway_view *view);
+
 /**
  * Map a view, ie. make it visible in the tree.
  *
diff --git a/include/sway/tree/workspace.h b/include/sway/tree/workspace.h
index 77991b275..27ed649fd 100644
--- a/include/sway/tree/workspace.h
+++ b/include/sway/tree/workspace.h
@@ -62,7 +62,9 @@ struct sway_workspace *workspace_create(struct sway_output *output,
 
 void workspace_destroy(struct sway_workspace *workspace);
 
-bool workspace_consider_destroy(struct sway_workspace *ws);
+void workspace_begin_destroy(struct sway_workspace *workspace);
+
+void workspace_consider_destroy(struct sway_workspace *ws);
 
 char *workspace_next_name(const char *output_name);
 
diff --git a/sway/commands/move.c b/sway/commands/move.c
index 8e52e4bc8..90e8585b4 100644
--- a/sway/commands/move.c
+++ b/sway/commands/move.c
@@ -611,16 +611,14 @@ static struct cmd_results *cmd_move_container(bool no_auto_back_and_forth,
 	if (old_parent) {
 		container_reap_empty(old_parent);
 	} else if (old_ws) {
-		if (workspace_consider_destroy(old_ws)) {
-			old_ws = NULL;
-		}
+		workspace_consider_destroy(old_ws);
 	}
 
 	// arrange windows
 	if (root->fullscreen_global) {
 		arrange_root();
 	} else {
-		if (old_ws) {
+		if (old_ws && !old_ws->node.destroying) {
 			arrange_workspace(old_ws);
 		}
 		arrange_node(node_get_parent(destination));
@@ -755,9 +753,7 @@ static struct cmd_results *cmd_move_in_direction(
 	if (old_parent) {
 		container_reap_empty(old_parent);
 	} else if (old_ws) {
-		if (workspace_consider_destroy(old_ws)) {
-			old_ws = NULL;
-		}
+		workspace_consider_destroy(old_ws);
 	}
 
 	struct sway_workspace *new_ws = container->pending.workspace;
@@ -765,9 +761,7 @@ static struct cmd_results *cmd_move_in_direction(
 	if (root->fullscreen_global) {
 		arrange_root();
 	} else {
-		if (old_ws) {
-			arrange_workspace(old_ws);
-		}
+		arrange_workspace(old_ws);
 		if (new_ws != old_ws) {
 			arrange_workspace(new_ws);
 		}
diff --git a/sway/desktop/launcher.c b/sway/desktop/launcher.c
index 5a330554a..2362e1ba0 100644
--- a/sway/desktop/launcher.c
+++ b/sway/desktop/launcher.c
@@ -153,7 +153,7 @@ static void ctx_handle_node_destroy(struct wl_listener *listener, void *data) {
 		// same output
 		free(ctx->fallback_name);
 		ctx->fallback_name = strdup(ws->name);
-		if (!ws->output) {
+		if (!ws->output || ws->output->node.destroying) {
 			// If the output is being destroyed it would be pointless to track
 			// If the output is being disabled, we'll find out if it's still
 			// disabled when we try to match it.
diff --git a/sway/desktop/output.c b/sway/desktop/output.c
index eeb203ffc..12dc9cc7a 100644
--- a/sway/desktop/output.c
+++ b/sway/desktop/output.c
@@ -428,7 +428,7 @@ void force_modeset(void) {
 	apply_stored_output_configs();
 }
 
-static void output_teardown(struct sway_output *output) {
+static void begin_destroy(struct sway_output *output) {
 
 	wl_list_remove(&output->layout_destroy.link);
 	wl_list_remove(&output->destroy.link);
@@ -444,6 +444,7 @@ static void output_teardown(struct sway_output *output) {
 	if (output->enabled) {
 		output_disable(output);
 	}
+	output_begin_destroy(output);
 	wl_list_remove(&output->link);
 
 	output->wlr_output->data = NULL;
@@ -452,19 +453,17 @@ static void output_teardown(struct sway_output *output) {
 	wl_event_source_remove(output->repaint_timer);
 	output->repaint_timer = NULL;
 
-	output_destroy(output);
-
 	request_modeset();
 }
 
 static void handle_destroy(struct wl_listener *listener, void *data) {
 	struct sway_output *output = wl_container_of(listener, output, destroy);
-	output_teardown(output);
+	begin_destroy(output);
 }
 
 static void handle_layout_destroy(struct wl_listener *listener, void *data) {
 	struct sway_output *output = wl_container_of(listener, output, layout_destroy);
-	output_teardown(output);
+	begin_destroy(output);
 }
 
 static void handle_present(struct wl_listener *listener, void *data) {
diff --git a/sway/desktop/transaction.c b/sway/desktop/transaction.c
index 73e860ea1..325a30226 100644
--- a/sway/desktop/transaction.c
+++ b/sway/desktop/transaction.c
@@ -59,6 +59,22 @@ static void transaction_destroy(struct sway_transaction *transaction) {
 		if (node->instruction == instruction) {
 			node->instruction = NULL;
 		}
+		if (node->destroying && node->ntxnrefs == 0) {
+			switch (node->type) {
+			case N_ROOT:
+				sway_assert(false, "Never reached");
+				break;
+			case N_OUTPUT:
+				output_destroy(node->sway_output);
+				break;
+			case N_WORKSPACE:
+				workspace_destroy(node->sway_workspace);
+				break;
+			case N_CONTAINER:
+				container_destroy(node->sway_container);
+				break;
+			}
+		}
 		free(instruction);
 	}
 	list_free(transaction->instructions);
@@ -223,7 +239,7 @@ static void apply_container_state(struct sway_container *container,
 
 	if (view) {
 		if (view->saved_surface_tree) {
-			if (container->node.ntxnrefs == 1) {
+			if (!container->node.destroying || container->node.ntxnrefs == 1) {
 				view_remove_saved_buffer(view);
 			}
 		}
@@ -772,6 +788,9 @@ static bool should_configure(struct sway_node *node,
 	if (!node_is_view(node)) {
 		return false;
 	}
+	if (node->destroying) {
+		return false;
+	}
 	if (!instruction->server_request) {
 		return false;
 	}
@@ -806,7 +825,7 @@ static void transaction_commit(struct sway_transaction *transaction) {
 		struct sway_transaction_instruction *instruction =
 			transaction->instructions->items[i];
 		struct sway_node *node = instruction->node;
-		bool hidden = node_is_view(node) &&
+		bool hidden = node_is_view(node) && !node->destroying &&
 			!view_is_visible(node->sway_container->view);
 		if (should_configure(node, instruction)) {
 			instruction->serial = view_configure(node->sway_container->view,
@@ -948,39 +967,3 @@ void transaction_commit_dirty(void) {
 void transaction_commit_dirty_client(void) {
 	_transaction_commit_dirty(false);
 }
-
-static void _transaction_remove_node(struct sway_transaction *transaction,
-		struct sway_node *node) {
-	if (!transaction || !node) {
-		return;
-	}
-	for (int idx = 0; idx < transaction->instructions->length; idx++) {
-		struct sway_transaction_instruction *instruction =
-			transaction->instructions->items[idx];
-		struct sway_node *n = instruction->node;
-		if (n != node) {
-			continue;
-		}
-
-		n->ntxnrefs--;
-		n->instruction = NULL;
-		free(instruction);
-		list_del(transaction->instructions, idx);
-		idx--;
-	}
-}
-
-void transaction_remove_node(struct sway_node *node) {
-	_transaction_remove_node(server.pending_transaction, node);
-	_transaction_remove_node(server.queued_transaction, node);
-
-	for (int idx = 0; idx < server.dirty_nodes->length; idx++) {
-		struct sway_node *n = server.dirty_nodes->items[idx];
-		if (n != node) {
-			continue;
-		}
-		n->dirty = false;
-		list_del(server.dirty_nodes, idx);
-		idx--;
-	}
-}
diff --git a/sway/desktop/xdg_shell.c b/sway/desktop/xdg_shell.c
index be19a5d6b..3852806e4 100644
--- a/sway/desktop/xdg_shell.c
+++ b/sway/desktop/xdg_shell.c
@@ -535,7 +535,7 @@ static void handle_destroy(struct wl_listener *listener, void *data) {
 	if (view->xdg_decoration) {
 		view->xdg_decoration->view = NULL;
 	}
-	view_destroy(view);
+	view_begin_destroy(view);
 }
 
 struct sway_view *view_from_wlr_xdg_surface(
diff --git a/sway/desktop/xwayland.c b/sway/desktop/xwayland.c
index fef0ff781..76e63ce1f 100644
--- a/sway/desktop/xwayland.c
+++ b/sway/desktop/xwayland.c
@@ -482,7 +482,7 @@ static void handle_destroy(struct wl_listener *listener, void *data) {
 	wl_list_remove(&xwayland_view->associate.link);
 	wl_list_remove(&xwayland_view->dissociate.link);
 	wl_list_remove(&xwayland_view->override_redirect.link);
-	view_destroy(&xwayland_view->view);
+	view_begin_destroy(&xwayland_view->view);
 }
 
 static void handle_unmap(struct wl_listener *listener, void *data) {
diff --git a/sway/tree/container.c b/sway/tree/container.c
index 2767bc231..0385d7c17 100644
--- a/sway/tree/container.c
+++ b/sway/tree/container.c
@@ -55,7 +55,7 @@ static void handle_destroy(
 	struct sway_container *con = wl_container_of(
 			listener, con, output_handler_destroy);
 
-	container_destroy(con);
+	container_begin_destroy(con);
 }
 
 static bool handle_point_accepts_input(
@@ -501,6 +501,36 @@ void container_update_title_bar(struct sway_container *con) {
 }
 
 void container_destroy(struct sway_container *con) {
+	if (!sway_assert(con->node.destroying,
+				"Tried to free container which wasn't marked as destroying")) {
+		return;
+	}
+	if (!sway_assert(con->node.ntxnrefs == 0, "Tried to free container "
+				"which is still referenced by transactions")) {
+		return;
+	}
+	free(con->title);
+	free(con->formatted_title);
+	free(con->title_format);
+	list_free(con->pending.children);
+	list_free(con->current.children);
+
+	list_free_items_and_destroy(con->marks);
+
+	if (con->view && con->view->container == con) {
+		con->view->container = NULL;
+		wlr_scene_node_destroy(&con->output_handler->node);
+		if (con->view->destroying) {
+			view_destroy(con->view);
+		}
+	}
+
+	scene_node_disown_children(con->content_tree);
+	wlr_scene_node_destroy(&con->scene_tree->node);
+	free(con);
+}
+
+void container_begin_destroy(struct sway_container *con) {
 	if (con->view) {
 		ipc_event_window(con, "close");
 	}
@@ -517,6 +547,9 @@ void container_destroy(struct sway_container *con) {
 
 	container_end_mouse_operation(con);
 
+	con->node.destroying = true;
+	node_set_dirty(&con->node);
+
 	if (con->scratchpad) {
 		root_scratchpad_remove_container(con);
 	}
@@ -534,28 +567,6 @@ void container_destroy(struct sway_container *con) {
 		wl_list_remove(&con->output_leave.link);
 		wl_list_remove(&con->output_handler_destroy.link);
 	}
-
-	transaction_remove_node(&con->node);
-	if (!sway_assert(con->node.ntxnrefs == 0, "Tried to free container "
-				"which is still referenced by transactions")) {
-		return;
-	}
-	free(con->title);
-	free(con->formatted_title);
-	free(con->title_format);
-	list_free(con->pending.children);
-	list_free(con->current.children);
-
-	list_free_items_and_destroy(con->marks);
-
-	if (con->view && con->view->container == con) {
-		con->view->container = NULL;
-		wlr_scene_node_destroy(&con->output_handler->node);
-	}
-
-	scene_node_disown_children(con->content_tree);
-	wlr_scene_node_destroy(&con->scene_tree->node);
-	free(con);
 }
 
 void container_reap_empty(struct sway_container *con) {
@@ -568,7 +579,7 @@ void container_reap_empty(struct sway_container *con) {
 			return;
 		}
 		struct sway_container *parent = con->pending.parent;
-		container_destroy(con);
+		container_begin_destroy(con);
 		con = parent;
 	}
 	if (ws) {
@@ -584,7 +595,7 @@ struct sway_container *container_flatten(struct sway_container *container) {
 		struct sway_container *child = container->pending.children->items[0];
 		struct sway_container *parent = container->pending.parent;
 		container_replace(container, child);
-		container_destroy(container);
+		container_begin_destroy(container);
 		container = parent;
 	}
 	return container;
diff --git a/sway/tree/output.c b/sway/tree/output.c
index b969c8105..b02c1a2ce 100644
--- a/sway/tree/output.c
+++ b/sway/tree/output.c
@@ -2,7 +2,6 @@
 #include <ctype.h>
 #include <string.h>
 #include <strings.h>
-#include "sway/desktop/transaction.h"
 #include "sway/ipc-server.h"
 #include "sway/layers.h"
 #include "sway/output.h"
@@ -236,7 +235,7 @@ static void output_evacuate(struct sway_output *output) {
 			}
 
 			if (workspace_num_sticky_containers(workspace) == 0) {
-				workspace_destroy(workspace);
+				workspace_begin_destroy(workspace);
 				continue;
 			}
 		}
@@ -254,6 +253,27 @@ static void output_evacuate(struct sway_output *output) {
 	}
 }
 
+void output_destroy(struct sway_output *output) {
+	if (!sway_assert(output->node.destroying,
+				"Tried to free output which wasn't marked as destroying")) {
+		return;
+	}
+	if (!sway_assert(output->wlr_output == NULL,
+				"Tried to free output which still had a wlr_output")) {
+		return;
+	}
+	if (!sway_assert(output->node.ntxnrefs == 0, "Tried to free output "
+				"which is still referenced by transactions")) {
+		return;
+	}
+
+	destroy_scene_layers(output);
+	list_free(output->workspaces);
+	list_free(output->current.workspaces);
+	wlr_color_transform_unref(output->color_transform);
+	free(output);
+}
+
 void output_disable(struct sway_output *output) {
 	if (!sway_assert(output->enabled, "Expected an enabled output")) {
 		return;
@@ -275,24 +295,15 @@ void output_disable(struct sway_output *output) {
 	output_evacuate(output);
 }
 
-void output_destroy(struct sway_output *output) {
+void output_begin_destroy(struct sway_output *output) {
 	if (!sway_assert(!output->enabled, "Expected a disabled output")) {
 		return;
 	}
+	sway_log(SWAY_DEBUG, "Destroying output '%s'", output->wlr_output->name);
 	wl_signal_emit_mutable(&output->node.events.destroy, &output->node);
 
-	transaction_remove_node(&output->node);
-
-	if (!sway_assert(output->node.ntxnrefs == 0, "Tried to free output "
-				"which is still referenced by transactions")) {
-		return;
-	}
-
-	destroy_scene_layers(output);
-	list_free(output->workspaces);
-	list_free(output->current.workspaces);
-	wlr_color_transform_unref(output->color_transform);
-	free(output);
+	output->node.destroying = true;
+	node_set_dirty(&output->node);
 }
 
 struct sway_output *output_from_wlr_output(struct wlr_output *output) {
diff --git a/sway/tree/view.c b/sway/tree/view.c
index d4f72211b..7bf185fea 100644
--- a/sway/tree/view.c
+++ b/sway/tree/view.c
@@ -70,10 +70,11 @@ bool view_init(struct sway_view *view, enum sway_view_type type,
 }
 
 void view_destroy(struct sway_view *view) {
-	if (!sway_assert(view->surface == NULL, "Tried to destroy a mapped view")) {
+	if (!sway_assert(view->surface == NULL, "Tried to free mapped view")) {
 		return;
 	}
-	if (!sway_assert(view->surface == NULL, "Tried to free mapped view")) {
+	if (!sway_assert(view->destroying,
+				"Tried to free view which wasn't marked as destroying")) {
 		return;
 	}
 	if (!sway_assert(view->container == NULL,
@@ -94,6 +95,17 @@ void view_destroy(struct sway_view *view) {
 	}
 }
 
+void view_begin_destroy(struct sway_view *view) {
+	if (!sway_assert(view->surface == NULL, "Tried to destroy a mapped view")) {
+		return;
+	}
+	view->destroying = true;
+
+	if (!view->container) {
+		view_destroy(view);
+	}
+}
+
 const char *view_get_title(struct sway_view *view) {
 	if (view->impl->get_string_prop) {
 		return view->impl->get_string_prop(view, VIEW_PROP_TITLE);
@@ -923,19 +935,17 @@ void view_unmap(struct sway_view *view) {
 
 	struct sway_container *parent = view->container->pending.parent;
 	struct sway_workspace *ws = view->container->pending.workspace;
-	container_destroy(view->container);
+	container_begin_destroy(view->container);
 	if (parent) {
 		container_reap_empty(parent);
 	} else if (ws) {
-		if (workspace_consider_destroy(ws)) {
-			ws = NULL;
-		}
+		workspace_consider_destroy(ws);
 	}
 
 	if (root->fullscreen_global) {
 		// Container may have been a child of the root fullscreen container
 		arrange_root();
-	} else if (ws) {
+	} else if (ws && !ws->node.destroying) {
 		arrange_workspace(ws);
 		workspace_detect_urgent(ws);
 	}
@@ -1089,6 +1099,9 @@ void view_update_title(struct sway_view *view, bool force) {
 }
 
 bool view_is_visible(struct sway_view *view) {
+	if (view->container->node.destroying) {
+		return false;
+	}
 	struct sway_workspace *workspace = view->container->pending.workspace;
 	if (!workspace && view->container->pending.fullscreen_mode != FULLSCREEN_GLOBAL) {
 		bool fs_global_descendant = false;
diff --git a/sway/tree/workspace.c b/sway/tree/workspace.c
index 44256bcff..f2be4cd13 100644
--- a/sway/tree/workspace.c
+++ b/sway/tree/workspace.c
@@ -5,7 +5,6 @@
 #include <stdio.h>
 #include <strings.h>
 #include "stringop.h"
-#include "sway/desktop/transaction.h"
 #include "sway/input/input-manager.h"
 #include "sway/input/cursor.h"
 #include "sway/input/seat.h"
@@ -135,15 +134,10 @@ struct sway_workspace *workspace_create(struct sway_output *output,
 }
 
 void workspace_destroy(struct sway_workspace *workspace) {
-	sway_log(SWAY_DEBUG, "Destroying workspace '%s'", workspace->name);
-	ipc_event_workspace(NULL, workspace, "empty"); // intentional
-	wl_signal_emit_mutable(&workspace->node.events.destroy, &workspace->node);
-
-	if (workspace->output) {
-		workspace_detach(workspace);
+	if (!sway_assert(workspace->node.destroying,
+				"Tried to free workspace which wasn't marked as destroying")) {
+		return;
 	}
-	transaction_remove_node(&workspace->node);
-
 	if (!sway_assert(workspace->node.ntxnrefs == 0, "Tried to free workspace "
 				"which is still referenced by transactions")) {
 		return;
@@ -164,25 +158,36 @@ void workspace_destroy(struct sway_workspace *workspace) {
 	free(workspace);
 }
 
-bool workspace_consider_destroy(struct sway_workspace *ws) {
+void workspace_begin_destroy(struct sway_workspace *workspace) {
+	sway_log(SWAY_DEBUG, "Destroying workspace '%s'", workspace->name);
+	ipc_event_workspace(NULL, workspace, "empty"); // intentional
+	wl_signal_emit_mutable(&workspace->node.events.destroy, &workspace->node);
+
+	if (workspace->output) {
+		workspace_detach(workspace);
+	}
+	workspace->node.destroying = true;
+	node_set_dirty(&workspace->node);
+}
+
+void workspace_consider_destroy(struct sway_workspace *ws) {
 	if (ws->tiling->length || ws->floating->length) {
-		return false;
+		return;
 	}
 
 	if (ws->output && output_get_active_workspace(ws->output) == ws) {
-		return false;
+		return;
 	}
 
 	struct sway_seat *seat;
 	wl_list_for_each(seat, &server.input->seats, link) {
 		struct sway_node *node = seat_get_focus_inactive(seat, &root->node);
 		if (node == &ws->node) {
-			return false;
+			return;
 		}
 	}
 
-	workspace_destroy(ws);
-	return true;
+	workspace_begin_destroy(ws);
 }
 
 static bool workspace_valid_on_output(const char *output_name,
@@ -591,6 +596,9 @@ bool workspace_switch(struct sway_workspace *workspace) {
 }
 
 bool workspace_is_visible(struct sway_workspace *ws) {
+	if (ws->node.destroying) {
+		return false;
+	}
 	return output_get_active_workspace(ws->output) == ws;
 }